CHAPTER 1

STRUCTURE AND BONDING

1.1 Atomic Structure
Atom:
Nucleus neutrons (neutral) + protons (+ve), the mass of the
atom.
Electron - Negatively charged, negligible mass
Atom is neutral,
No. of protons = no. of electrons
Diameter of an atom is about 2 10
-10
m (200
picometers (pm)) [the unit angstrom () is 10
-10
m =
100 pm]
Atomic number (Z) - number of protons in the
atom's nucleus
Mass number (A) - number of protons plus
neutrons
Atoms of a given element have the same atomic
number:
1 for hydrogen, H
6 for carbon, C
Isotopes - atoms of the same element but
different numbers of neutrons different mass
numbers
Atomic mass (atomic weight) - weighted
average mass in atomic mass units (amu) of an
elements naturally occurring isotopes
1.2 Atomic Structure: Orbitals
4 kinds of orbitals: s, p, d, and f







Orbitals are organised into different layers
electron shells

Orbitals and Shells
Orbitals are grouped in shells of increasing size and energy
Different shells contain different numbers and kinds of orbitals
Each orbital can be occupied by two electrons
First shell contains one s orbital, denoted 1s, holds only two
electrons
Second shell contains one s orbital (2s) and three p orbitals (2p),
eight electrons
Third shell contains an s orbital (3s), three p orbitals (3p), and five d
orbitals (3d), 18 electrons

p-Orbitals
3 p orbitals within a given shell are oriented in
perpendicular directions: p
x
, p
y
, and p
z

Lobes of a p orbital are separated by region of zero
electron density, a node
1.3 Atomic Structure: Electron
Configurations
Ground-state electron configuration (lowest
energy arrangement) listing of orbitals
occupied by the electrons.

Rules 1:
Lowest-energy orbitals
first: 1s 2s 2p
3s 3p 4s 3d
(Aufbau (build-up)
principle)

Rules 2:
Electrons act as they are
spinning around axis,
2 spin orientations: or

Only 2 electrons occupy
an orbital
Pauli exclusion
principle
Rules 3:
If 2 or more empty orbitals
of equal energy are
available, 1 electron
occupies with parallel
spins until orbitals are
half-full
Hunds rule
1.4 Development of Chemical Bonding
Theory
Atoms form bonds because the compound that
results is more stable than the separate atoms
Ionic bonds in salts form as a result of electron
transfers (example: Na
+
Cl
-
)
Organic compounds have covalent bonds from
sharing electrons (G. N. Lewis, 1916)
Kekul and Couper independently observed that
carbon always has four bonds

van't Hoff and Le Bel proposed that the four bonds of
carbon have specific spatial directions
Atoms surround carbon as corners of a tetrahedron
Lewis structures (electron dot) show valence electrons of
an atom as dots
Hydrogen has one dot, representing its 1s electron
Carbon has four dots (2s
2
2p
2
)




Kekule structures (line-bond structures) have a line drawn
between two atoms indicating a 2 electron covalent bond.


Method of indicating covalent bonds
Note that:

Stable molecule = noble gas configuration
completed shell, octet (eight dots) for main-group atoms, two
for hydrogen
Depends on how many additional valence electrons to
reach noble-gas configuration.
Carbon has four valence electrons (2s
2
2p
2
), forming four
bonds (CH
4
).
Nitrogen has five valence electrons (2s
2
2p
3
) but forms only
three bonds (NH
3
).
Oxygen has six valence electrons (2s
2
2p
4
) but forms two
bonds (H
2
O)

Nonbonding electron
Valence electrons not used in bonding are called
nonbonding electrons, or lone-pair electrons
Nitrogen atom in ammonia (NH
3
)
Shares six valence electrons in three covalent bonds and
remaining two valence electrons are nonbonding lone pair
Drawing Structures
Drawing every bond in organic molecule can
become tedious.
Several shorthand methods have been developed to
write structures.
1)Condensed structures dont have C-H or C-C single
bonds shown. They are understood.
2)Skeletal structures


Skeletal structure
3 General Rules:
1) Carbon atoms arent usually shown. Instead a
carbon atom is assumed to be at each
intersection of two lines (bonds) and at the end
of each line.

2) Hydrogen atoms bonded to carbon arent
shown.

3) Atoms other than carbon and hydrogen are
shown.
1.5 The Nature of Chemical Bonds:
Valence Bond Theory
2 models to describe covalent bonding:
Valence bond theory
Molecular orbital theory
Covalent bond forms when two atoms approach each
other closely so that a singly occupied orbital on one
atom overlaps a singly occupied orbital on the other atom



H-H bond is cylindrically symmetrical, bond formed by the
head-on overlap of 2 atomic orbitals are called sigma ()
bonds

Bond Energy
Reaction 2 H H
2
releases 436 kJ/mol
Product has 436 kJ/mol less energy than two
atoms: HH has bond strength of 436 kJ/mol.
(1 kJ = 0.2390 kcal; 1 kcal = 4.184 kJ)
Bond Length
Distance between
nuclei that leads
to maximum
stability
If too close, they
repel because
both are positively
charged
If too far apart,
bonding is weak
1.6 sp
3
Orbitals
Carbon has 4 valence electrons (2s
2
2p
2
)
In CH
4
, all CH bonds are identical (tetrahedral)
sp
3
hybrid orbitals: s orbital and three p orbitals
combine to form four equivalent, unsymmetrical,
tetrahedral orbitals (sppp = sp
3
), Pauling (1931)
Structure of methane

sp
3
orbitals on C overlap with 1s orbitals on 4 H
atoms to form four identical C-H bonds
Each CH bond has a strength of 436 (438)
kJ/mol and length of 109 pm
Bond angle bonds specific geometry,
methane: each HCH is 109.5, the tetrahedral
angle.
Structure of ethane

Two Cs bond to each other by overlap of an sp
3

orbital from each
Three sp
3
orbitals on each C overlap with H 1s
orbitals to form six CH bonds
CH bond strength in ethane 423 kJ/mol
CC bond is 154 pm long and strength is 376 kJ/mol
All bond angles of ethane are tetrahedral value of
109.5
1.7 sp
2
Orbitals
sp
2
hybrid orbitals: 2s orbital combines with two 2p
orbitals, giving 3 orbitals (spp = sp
2
). This results in a
double bond.
sp
2
orbitals are in a plane with120 angles
Remaining p orbital is perpendicular to the plane
Bonds from sp
2
hybrid orbitals

Two sp
2
-hybridized orbitals overlap to form a
bond
p orbitals overlap side-to-side to format a pi ()
bond
sp
2
sp
2
bond and 2p2p bond result in
sharing four electrons and formation of C-C
double bond
Electrons in the bond are centered between
nuclei
Electrons in the bond occupy regions are on
either side of a line between nuclei
Structure of ethylene

H atoms form bonds with four sp
2
orbitals
HCH and HCC bond angles of about 120
CC double bond in ethylene shorter and stronger
than single bond in ethane
Ethylene C=C bond length 134 pm (CC 154 pm)
1.8 sp

Orbitals
C-C a triple bond sharing six electrons
Carbon 2s orbital hybridizes with a single p
orbital giving two sp hybrids
two p orbitals remain unchanged
sp orbitals are linear, 180 apart on x-axis
Two p orbitals are perpendicular on the y-axis
and the z-axis
Orbitals of acetylene

Two sp hybrid orbitals from each C form spsp
bond
p
z
orbitals from each C form a p
z
p
z
bond by
sideways overlap and p
y
orbitals overlap similarly
Bonding in acetylene

Sharing of six electrons forms C C

Two sp orbitals form bonds with hydrogens
Comparison of C-C and C-H
bonds
1.9 Hybridization of Nitrogen and
Oxygen
Elements other than C can have hybridized orbitals
HNH bond angle in ammonia (NH
3
) 107.3
C-N-H bond angle is 110.3
Ns orbitals (sppp) hybridize to form four sp
3
orbitals
One sp
3
orbital is occupied by two nonbonding
electrons, and three sp
3
orbitals have one electron
each, forming bonds to H and CH
3
.
1.10 The nature of chemical
bonds: Molecular Orbital Theory
A molecular orbital (MO): where electrons are most
likely to be found (specific energy and general
shape) in a molecule
Additive combination (bonding) MO is lower in
energy
Subtractive combination (antibonding) MO is higher
energy
Molecular Orbitals in Ethylene
The bonding MO is from combining p orbital
lobes with the same algebraic sign
The antibonding MO is from combining lobes
with opposite signs
Only bonding MO is occupied
Summary
Organic chemistry chemistry of carbon compounds
Atom: positively charged nucleus surrounded by
negatively charged electrons
Electronic structure of an atom described by wave
equation
Electrons occupy orbitals around the nucleus.
Different orbitals have different energy levels and different
shapes
s orbitals are spherical, p orbitals are dumbbell-shaped
Covalent bonds - electron pair is shared between atoms
Valence bond theory - electron sharing occurs by
overlap of two atomic orbitals
Molecular orbital (MO) theory, - bonds result from
combination of atomic orbitals to give molecular orbitals,
which belong to the entire molecule
Sigma () bonds - Circular cross-section and are formed
by head-on interaction
Pi () bonds dumbbell shape from sideways
interaction of p orbitals



Carbon uses hybrid orbitals to form bonds in organic
molecules.
In single bonds with tetrahedral geometry, carbon has four
sp
3
hybrid orbitals
In double bonds with planar geometry, carbon uses three
equivalent sp
2
hybrid orbitals and one unhybridized p
orbital
Carbon uses two equivalent sp hybrid orbitals to form a
triple bond with linear geometry, with two unhybridized p
orbitals
Atoms such as nitrogen and oxygen hybridize to form
strong, oriented bonds
The nitrogen atom in ammonia and the oxygen atom in
water are sp
3
-hybridized